Scaffold PTM

What’s new in Scaffold PTM 3.0

Label Free Quantitation
It is now possible to load precursor intensity ratios exported from Scaffold Q+/Q+S into Scaffold PTM .

Modification Site Quantitation Normalized by Protein Expression with Scatter Plot
Normalize differences in PTM expression by corresponding differences in protein expression.
Samples must be analyzed in parallel for protein and PTM expression using Scaffold Q+/Q+S.

Statistical Analysis of PTM Site Quantitation Ratios with Volcano Plot
This feature provides a confidence assessment that the expression levels
are significantly different at any level of summarization, with or without
protein expression normalization.

Motif Analysis of Selected Peptides
This new extension of the Scaffold PTM motif search allows users to define
a set of PTM peptides to be searched against a custom-defined background,
and includes the option to use the remaining peptides as the background.

Publish View
This view provides information about the data loaded into Scaffold PTM and the analyses performed.

Gene Ontology AnnotationsGO terms may now be added to the PTM List table.

Modification FilteringSelect which modification types should be displayed and export filtered reports.